BAFfromGenotypes {GWASTools} | R Documentation

## B Allele Frequency & Log R Ratio Calculation

### Description

This function calculates the B allele frequency and the log R ratio values for samples by either plate or by study.

### Usage

    BAFfromGenotypes(intenData, genoData,
                     filename, file.type = c("gds", "ncdf"),
                     min.n.genotypes = 2,
                     call.method = c("by.plate", "by.study"),
                     plate.name = "plate",
                     block.size = 5000,
    	         precision="single", compress="LZMA_RA:1M",
                     verbose = TRUE)

### Arguments

`intenData` | `IntensityData` object holding the X and Y intensity data from which the B allele frequency and log R ratio are calculated.
`genoData` | `GenotypeData` object.
`filename` | The name of the genotype GDS or netCDF file to create
`file.type` | The type of file to create ("gds" or "ncdf")
`min.n.genotypes` | The minimum number of samples for each genotype at any SNP in order to have non-missing B allele freqency and log R ratio. Setting this parameter to 2 or a similar value is recommended.
`call.method` | If call.method is 'by.plate', the B allele frequency and log R ratio are calculated for samples delineated by plates. This is the default method. If call.method is 'by.study', the calculation uses all samples at once. If a study does not have plate specifications, 'by.study' is the call.method that must be used.
`plate.name` | Character string specifying the name of the plate variable in intenData or genoData. By default, the plate.name is simply 'plate' but oftentimes there are variations, such as 'plateID' or 'plate.num'.
`block.size` | An integer specifying the number of SNPs to be loaded at one time. The recommended value is around 1000, but should vary depending on computing power.
`precision` | A character value indicating whether floating point numbers should be stored as "double" or "single" precision.
`compress` | The compression level for variables in a GDS file (see `add.gdsn` for options.
`verbose` | Logical value specifying whether to show progress information.

### Details

Because this function can take a considerable amount of time and space, sufficient attention should be given to the value used for `block.size`.

### Author(s)

Caitlin McHugh

### References

Peiffer D.A., Le J.M., Steemers F.J., Chang W., Jenniges T., and et al. High-resolution genomic profiling of chromosomal aberrations using infinium whole-genome genotyping. Genome Research, 16:1136-1148, 2006.

### See Also

`IntensityData`, `GenotypeData`, `chromIntensityPlot`, `BAFfromClusterMeans`

### Examples

    ## Not run:
    # create IntensityData and GenotypeData objects from netCDF
    library(GWASdata)
    data(affySnpADF)
    data(affyScanADF)
    nsamp <- nrow(affyScanADF)

    xyfile <- system.file("extdata", "affy_qxy.nc", package="GWASdata")
    xyNC <- NcdfIntensityReader(xyfile)
    xyData <- IntensityData(xyNC, snpAnnot=affySnpADF, scanAnnot=affyScanADF)

    genofile <- system.file("extdata", "affy_geno.nc", package="GWASdata")
    genoNC <- NcdfGenotypeReader(genofile)
    genoData <- GenotypeData(genoNC, snpAnnot=affySnpADF, scanAnnot=affyScanADF)

    # calculate BAF and LRR
    blfile <- tempfile()
    BAFfromGenotypes(xyData, genoData, blfile, file.type="ncdf", min.n.genotypes=2,
                     call.method="by.plate", plate.name="plate")

    blNC <- NcdfIntensityReader(blfile)
    baf <- getBAlleleFreq(blNC)
    lrr <- getLogRRatio(blNC)

    close(xyData)
    close(genoData)
    close(blNC)
    file.remove(blfile)

    ## End(Not run)

[Package GWASTools version 1.26.1 Index]